Deciphering the Code for Retroviral Integration Target Site Selection

Upon cell invasion, retroviruses generate a DNA copy of their RNA genome and integrate retroviral cDNA within host chromosomal DNA. Integration occurs throughout the host cell genome, but target site selection is not random. Each subgroup of retrovirus is distinguished from the others by attraction to particular features on chromosomes. Despite extensive efforts to identify host factors that interact with retrovirion components or chromosome features predictive of integration, little is known about how integration sites are selected. We attempted to identify markers predictive of retroviral integration by exploiting Precision-Recall methods for extracting information from highly skewed datasets to derive robust and discriminating measures of association. ChIPSeq datasets for more than 60 factors were compared with 14 retroviral integration datasets. When compared with MLV, PERV or XMRV integration sites, strong association was observed with STAT1, acetylation of H3 and H4 at several positions, and methylation of H2AZ, H3K4, and K9. By combining peaks from ChIPSeq datasets, a supermarker was identified that localized within 2 kB of 75% of MLV proviruses and detected differences in integration preferences among different cell types. The supermarker predicted the likelihood of integration within specific chromosomal regions in a cell-type specific manner, yielding probabilities for integration into proto-oncogene LMO2 identical to experimentally determined values. The supermarker thus identifies chromosomal features highly favored for retroviral integration, provides clues to the mechanism by which retrovirus integration sites are selected, and offers a tool for predicting cell-type specific proto-oncogene activation by retroviruses

Closed hydroponic systems : operational parameters, root exudates occurrence and related water treatment

Greenhouse production of vegetables in closed hydroponic cropping systems is a resource-efficient technique for the production of high-quality produce with a high yield per unit area. Recently, there have been considerable progresses in the development of hydroponic culture. While this type of cropping system allows savings in terms of water and nutrient use, the recirculation of water increases the risk of root exudates dispersal. Plant roots often exude numerous organic acids, which are known to inhibit growth. So far several methods have been found to be effective in removing or degrading the phytotoxic substances released from plant roots during autotoxicity such as adsorption by activated carbon, electrodegradation of root exudates and TiO2 photocatalysis. In this review an overview will be presented of hydroponic systems and their related root exudates occurrence and removal

The DUNE Far Detector Interim Design Report Volume 1: Physics, Technology and Strategies

The DUNE IDR describes the proposed physics program and technical designs of the DUNE Far Detector modules in preparation for the full TDR to be published in 2019. It is intended as an intermediate milestone on the path to a full TDR, justifying the technical choices that flow down from the high-level physics goals through requirements at all levels of the Project. These design choices will enable the DUNE experiment to make the ground-breaking discoveries that will help to answer fundamental physics questions. Volume 1 contains an executive summary that describes the general aims of this document. The remainder of this first volume provides a more detailed description of the DUNE physics program that drives the choice of detector technologies. It also includes concise outlines of two overarching systems that have not yet evolved to consortium structures: computing and calibration. Volumes 2 and 3 of this IDR describe, for the single-phase and dual-phase technologies, respectively, each detector module's subsystems, the technical coordination required for its design, construction, installation, and integration, and its organizational structure

The DUNE Far Detector Interim Design Report, Volume 3: Dual-Phase Module

The DUNE IDR describes the proposed physics program and technical designs of the DUNE far detector modules in preparation for the full TDR to be published in 2019. It is intended as an intermediate milestone on the path to a full TDR, justifying the technical choices that flow down from the high-level physics goals through requirements at all levels of the Project. These design choices will enable the DUNE experiment to make the ground-breaking discoveries that will help to answer fundamental physics questions. Volume 3 describes the dual-phase module's subsystems, the technical coordination required for its design, construction, installation, and integration, and its organizational structure

The DUNE Far Detector Interim Design Report, Volume 2: Single-Phase Module

The DUNE IDR describes the proposed physics program and technical designs of the DUNE far detector modules in preparation for the full TDR to be published in 2019. It is intended as an intermediate milestone on the path to a full TDR, justifying the technical choices that flow down from the high-level physics goals through requirements at all levels of the Project. These design choices will enable the DUNE experiment to make the ground-breaking discoveries that will help to answer fundamental physics questions. Volume 2 describes the single-phase module's subsystems, the technical coordination required for its design, construction, installation, and integration, and its organizational structure